# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May  3 07:20:12 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: (2R,4R)-1-[(3-chloro-2-fluorophenyl)methyl]-4-({3-fluoro-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyridin-2-yl}methyl)-2-methylpiperidine-4-carboxylic acid
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: C[C@@H]1C[C@](CCN1Cc2cccc(Cl)c2F)(Cc3nc(Nc4cc(C)[nH]n4)ccc3F)C(O)=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 EG7  EG7  '(2R,4R)-1-[(3-chloro-2-fluorophenyl)methyl]-4-({3-fluoro-6-[(5-methyl-1H-pyrazol-3-yl)amino]pyridin-2-yl}methyl)-2-methylpiperidine-4-carboxylic acid'  ligand  60  34  .  2022-07-24  2023-02-16
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as OK (reasonable std)
;

data_comp_EG7
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 EG7  C7   C   CR6   0  -0.107  -3.0667  -0.3601   0.6843
 EG7  C6   C   CR15  0  -0.572   1.1289  -4.1925  -0.4173
 EG7  C1   C   CR16  0  -0.269  -3.8121  -2.4492  -0.2909
 EG7  C5   C   CR16  0  -0.387   4.9607  -1.3270  -0.8503
 EG7  C4   C   CR16  0  -0.222  -4.7277  -1.7772  -1.0845
 EG7  C3   C   CR16  0  -0.296   5.4058  -0.0242  -0.8400
 EG7  C2   C   CR16  0  -0.263  -2.9930  -1.7442   0.5800
 EG7  C8   C   CR6   0   0.436   4.6104   0.9412  -0.2463
 EG7  C9   C   CR6   0   0.624  -3.9920   0.2921  -0.1167
 EG7  C10  C   CR6   0  -0.229  -4.8156  -0.3967  -0.9914
 EG7  C11  C   CR6   0   0.089   3.3990   0.6007   0.3202
 EG7  C12  C   CR5   0   0.413   0.1025  -4.3834   0.4814
 EG7  C13  C   CR6   0   0.473   3.7198  -1.6074  -0.2531
 EG7  C14  C   CR5   0   0.482   2.0268  -3.3309   0.2458
 EG7  C15  C   C     0   0.592   2.1590   3.1857  -0.9033
 EG7  C16  C   CH2   0  -0.414   0.6152   1.1932  -0.7575
 EG7  C17  C   CH2   0  -0.400   0.4284   3.0456   0.8687
 EG7  C18  C   CH2   0  -0.298  -0.2898   0.3844   0.1504
 EG7  C19  C   CH1   0  -0.063  -0.5168   2.1952   1.7209
 EG7  C20  C   CT    0  -0.248   1.4188   2.2349   0.0234
 EG7  C22  C   CH3   0  -0.688  -1.4719   3.1373   2.4484
 EG7  C23  C   CH2   0  -0.337  -2.1742   0.4213   1.6108
 EG7  C24  C   CH2   0  -0.510   2.4831   1.5986   0.9645
 EG7  N25  N   N     0  -0.428   2.9877  -0.6662   0.3126
 EG7  N26  N   N     0  -0.290   1.5962  -3.0166   1.4507
 EG7  N27  N   NR15  0  -0.491   0.4275  -3.6505   1.5608
 EG7  N28  N   NT    0  -0.412  -1.2223   1.2339   0.8760
 EG7  N29  N   NH1   0  -0.774   3.2505  -2.8991  -0.2524
 EG7  O31  O   OH1   0  -0.588   2.5644   2.6091  -2.0272
 EG7  F33  F   F     0  -0.287  -4.1143   1.6184  -0.0371
 EG7  CL1  CL  CL    0  -0.097  -5.9451   0.4831  -1.9527
 EG7  H40  H   HCR5  0   0.263   1.2191  -4.6071  -1.4081
 EG7  H35  H   HCR6  0   0.266  -3.7378  -3.5260  -0.3599
 EG7  H39  H   HCR6  0   0.279   5.5546  -2.1100  -1.3037
 EG7  H38  H   HCR6  0   0.288  -5.3691  -2.3144  -1.7695
 EG7  H37  H   HCR6  0   0.289   6.3569   0.2424  -1.2827
 EG7  H36  H   HCR6  0   0.249  -2.2695  -2.2724   1.1884
 EG7  H41  H   HCH2  0   0.249   1.2614   0.5097  -1.3062
 EG7  H42  H   HCH2  0   0.236  -0.0099   1.7064  -1.4942
 EG7  H44  H   HCH2  0   0.238  -0.1857   3.6626   0.2049
 EG7  H43  H   HCH2  0   0.241   0.9649   3.7283   1.5307
 EG7  H45  H   HCH2  0   0.243  -0.8564  -0.3045  -0.4790
 EG7  H46  H   HCH2  0   0.221   0.3085  -0.2457   0.8278
 EG7  H47  H   HCH1  0   0.198   0.0737   1.6671   2.4919
 EG7  H49  H   HCH3  0   0.266  -0.9613  -6.2100   0.8142
 EG7  H48  H   HCH3  0   0.248  -1.9524  -4.7672   0.9621
 EG7  H50  H   HCH3  0   0.261  -1.4468  -5.3299  -0.6298
 EG7  H51  H   HCH3  0   0.227  -2.1933   3.5669   1.7509
 EG7  H52  H   HCH3  0   0.236  -2.0219   2.6513   3.2534
 EG7  H53  H   HCH3  0   0.237  -0.9085   3.9545   2.8997
 EG7  H55  H   HCH2  0   0.265  -2.7990   1.0628   2.2316
 EG7  H54  H   HCH2  0   0.221  -1.6741  -0.2840   2.2957
 EG7  H57  H   HCH2  0   0.275   1.9594   1.0722   1.7618
 EG7  H56  H   HCH2  0   0.269   3.0493   2.4015   1.4414
 EG7  H58  H   HNR5  0   0.413  -0.0981  -3.5660   2.4160
 EG7  H59  H   HNH1  0   0.404   3.7075  -3.5340  -0.8857
 EG7  H60  H   HOH1  0   0.479   3.0620   3.2462  -2.5619
 EG7  O30  O   O     0  -0.443   2.3880   4.3430  -0.6482
 EG7  F32  F   F     0  -0.317   5.0301   2.2215  -0.2227
 EG7  C21  C   CH3   0  -0.739  -1.1288  -5.2129   0.4041

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 EG7  N27  N26  aromatic  1.334  0.020  1.334
 EG7  N27  C12  aromatic  1.345  0.020  1.345
 EG7  N26  C14  aromatic  1.318  0.020  1.318
 EG7  C21  C12  single    1.487  0.020  1.487
 EG7  CL1  C10  single    1.724  0.020  1.724
 EG7  C12  C6   aromatic  1.378  0.020  1.378
 EG7  C14  C6   aromatic  1.410  0.020  1.410
 EG7  C14  N29  single    1.390  0.020  1.390
 EG7  C10  C4   aromatic  1.386  0.020  1.386
 EG7  C10  C9   aromatic  1.385  0.020  1.385
 EG7  C4   C1   aromatic  1.386  0.020  1.386
 EG7  N29  C13  single    1.374  0.020  1.374
 EG7  F33  C9   single    1.334  0.020  1.334
 EG7  C9   C7   aromatic  1.387  0.020  1.387
 EG7  C1   C2   aromatic  1.388  0.020  1.388
 EG7  C13  C5   aromatic  1.405  0.020  1.405
 EG7  C13  N25  aromatic  1.320  0.020  1.320
 EG7  C5   C3   aromatic  1.377  0.020  1.377
 EG7  C7   C2   aromatic  1.390  0.020  1.390
 EG7  C7   C23  single    1.505  0.020  1.505
 EG7  N25  C11  aromatic  1.332  0.020  1.332
 EG7  C18  C16  single    1.516  0.020  1.516
 EG7  C18  N28  single    1.455  0.020  1.455
 EG7  C23  N28  single    1.451  0.020  1.451
 EG7  C3   C8   aromatic  1.385  0.020  1.385
 EG7  C11  C8   aromatic  1.380  0.020  1.380
 EG7  C11  C24  single    1.500  0.020  1.500
 EG7  C16  C20  single    1.530  0.020  1.530
 EG7  N28  C19  single    1.461  0.020  1.461
 EG7  C8   F32  single    1.348  0.020  1.348
 EG7  C24  C20  single    1.557  0.020  1.557
 EG7  C20  C17  single    1.534  0.020  1.534
 EG7  C20  C15  single    1.520  0.020  1.520
 EG7  C19  C17  single    1.531  0.020  1.531
 EG7  C19  C22  single    1.526  0.020  1.526
 EG7  O31  C15  single    1.327  0.020  1.327
 EG7  C15  O30  double    1.207  0.020  1.207
 EG7  C6   H40  single    0.930  0.020  1.080
 EG7  C1   H35  single    0.930  0.020  1.080
 EG7  C5   H39  single    0.930  0.020  1.080
 EG7  C4   H38  single    0.930  0.020  1.080
 EG7  C3   H37  single    0.930  0.020  1.080
 EG7  C2   H36  single    0.930  0.020  1.080
 EG7  C16  H41  single    0.970  0.020  1.090
 EG7  C16  H42  single    0.970  0.020  1.090
 EG7  C17  H44  single    0.970  0.020  1.090
 EG7  C17  H43  single    0.970  0.020  1.090
 EG7  C18  H45  single    0.970  0.020  1.090
 EG7  C18  H46  single    0.970  0.020  1.090
 EG7  C19  H47  single    0.970  0.020  1.090
 EG7  C21  H49  single    0.970  0.020  1.090
 EG7  C21  H48  single    0.970  0.020  1.090
 EG7  C21  H50  single    0.970  0.020  1.090
 EG7  C22  H51  single    0.970  0.020  1.090
 EG7  C22  H52  single    0.970  0.020  1.090
 EG7  C22  H53  single    0.970  0.020  1.090
 EG7  C23  H55  single    0.970  0.020  1.090
 EG7  C23  H54  single    0.970  0.020  1.090
 EG7  C24  H57  single    0.970  0.020  1.090
 EG7  C24  H56  single    0.970  0.020  1.090
 EG7  N27  H58  single    0.860  0.020  1.020
 EG7  N29  H59  single    0.860  0.020  1.020
 EG7  O31  H60  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 EG7  C23  C7   C9   120.46  3.000
 EG7  C23  C7   C2   122.12  3.000
 EG7  C9   C7   C2   117.41  3.000
 EG7  H40  C6   C14  127.88  3.000
 EG7  H40  C6   C12  127.50  3.000
 EG7  C14  C6   C12  104.62  3.000
 EG7  H35  C1   C2   120.35  3.000
 EG7  H35  C1   C4   119.45  3.000
 EG7  C2   C1   C4   120.20  3.000
 EG7  H39  C5   C13  121.21  3.000
 EG7  H39  C5   C3   120.69  3.000
 EG7  C13  C5   C3   118.10  3.000
 EG7  H38  C4   C10  119.97  3.000
 EG7  H38  C4   C1   120.92  3.000
 EG7  C10  C4   C1   119.11  3.000
 EG7  H37  C3   C8   120.56  3.000
 EG7  H37  C3   C5   120.93  3.000
 EG7  C8   C3   C5   118.51  3.000
 EG7  H36  C2   C1   119.94  3.000
 EG7  H36  C2   C7   118.62  3.000
 EG7  C1   C2   C7   121.44  3.000
 EG7  F32  C8   C11  120.04  3.000
 EG7  F32  C8   C3   119.41  3.000
 EG7  C11  C8   C3   120.55  3.000
 EG7  F33  C9   C10  118.53  3.000
 EG7  F33  C9   C7   119.62  3.000
 EG7  C10  C9   C7   121.85  3.000
 EG7  CL1  C10  C9   119.20  3.000
 EG7  C9   C10  C4   119.99  3.000
 EG7  CL1  C10  C4   120.81  3.000
 EG7  N25  C11  C24  116.53  3.000
 EG7  C24  C11  C8   123.24  3.000
 EG7  N25  C11  C8   120.23  3.000
 EG7  N27  C12  C21  123.10  3.000
 EG7  C21  C12  C6   131.34  3.000
 EG7  N27  C12  C6   105.55  3.000
 EG7  N29  C13  N25  118.73  3.000
 EG7  N25  C13  C5   121.98  3.000
 EG7  N29  C13  C5   119.29  3.000
 EG7  N29  C14  N26  122.78  3.000
 EG7  N29  C14  C6   125.58  3.000
 EG7  N26  C14  C6   111.57  3.000
 EG7  O31  C15  O30  122.54  3.000
 EG7  O30  C15  C20  124.29  3.000
 EG7  O31  C15  C20  113.16  3.000
 EG7  H42  C16  H41  107.10  3.000
 EG7  H42  C16  C20  108.93  3.000
 EG7  H41  C16  C20  111.89  3.000
 EG7  H42  C16  C18  108.21  3.000
 EG7  H41  C16  C18  108.74  3.000
 EG7  C20  C16  C18  111.79  3.000
 EG7  H43  C17  H44  106.91  3.000
 EG7  H43  C17  C20  110.33  3.000
 EG7  H44  C17  C20  109.02  3.000
 EG7  H43  C17  C19  108.26  3.000
 EG7  H44  C17  C19  107.71  3.000
 EG7  C20  C17  C19  114.32  3.000
 EG7  H46  C18  H45  105.98  3.000
 EG7  H46  C18  N28  112.04  3.000
 EG7  H45  C18  N28  108.86  3.000
 EG7  H46  C18  C16  110.44  3.000
 EG7  H45  C18  C16  107.54  3.000
 EG7  N28  C18  C16  111.70  3.000
 EG7  H47  C19  N28  110.30  3.000
 EG7  H47  C19  C22  107.26  3.000
 EG7  N28  C19  C22  112.31  3.000
 EG7  H47  C19  C17  108.90  3.000
 EG7  C22  C19  C17  107.99  3.000
 EG7  N28  C19  C17  109.98  3.000
 EG7  C24  C20  C17  108.92  3.000
 EG7  C17  C20  C16  107.58  3.000
 EG7  C24  C20  C16  112.91  3.000
 EG7  C17  C20  C15  108.65  3.000
 EG7  C24  C20  C15  106.94  3.000
 EG7  C16  C20  C15  111.75  3.000
 EG7  H53  C22  H52  106.82  3.000
 EG7  H53  C22  H51  108.12  3.000
 EG7  H52  C22  H51  108.30  3.000
 EG7  H53  C22  C19  109.67  3.000
 EG7  H52  C22  C19  113.13  3.000
 EG7  H51  C22  C19  110.61  3.000
 EG7  H54  C23  H55  106.42  3.000
 EG7  H54  C23  N28  112.02  3.000
 EG7  H55  C23  N28  109.57  3.000
 EG7  H54  C23  C7   108.61  3.000
 EG7  H55  C23  C7   108.45  3.000
 EG7  N28  C23  C7   111.59  3.000
 EG7  H56  C24  H57  106.55  3.000
 EG7  H56  C24  C20  108.54  3.000
 EG7  H57  C24  C20  108.14  3.000
 EG7  H56  C24  C11  111.11  3.000
 EG7  H57  C24  C11  106.65  3.000
 EG7  C20  C24  C11  115.45  3.000
 EG7  C13  N25  C11  120.63  3.000
 EG7  N27  N26  C14  104.39  3.000
 EG7  H58  N27  N26  119.16  3.000
 EG7  H58  N27  C12  126.95  3.000
 EG7  N26  N27  C12  113.86  3.000
 EG7  C23  N28  C19  113.09  3.000
 EG7  C19  N28  C18  111.28  3.000
 EG7  C23  N28  C18  110.24  3.000
 EG7  H59  N29  C14  115.42  3.000
 EG7  H59  N29  C13  115.95  3.000
 EG7  C14  N29  C13  126.35  3.000
 EG7  H60  O31  C15  109.78  3.000
 EG7  H50  C21  H48  108.04  3.000
 EG7  H50  C21  H49  107.68  3.000
 EG7  H48  C21  H49  107.29  3.000
 EG7  H50  C21  C12  110.58  3.000
 EG7  H48  C21  C12  111.78  3.000
 EG7  H49  C21  C12  111.29  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 EG7  CONST_01  C4   C10  C9   C7      0.00   0.0  0
 EG7  CONST_02  C4   C1   C2   C7      0.00   0.0  0
 EG7  CONST_03  N26  N27  C12  C6      0.00   0.0  0
 EG7  CONST_04  N27  N26  C14  C6      0.00   0.0  0
 EG7  CONST_05  C9   C10  C4   C1      0.00   0.0  0
 EG7  CONST_06  C9   C7   C2   C1      0.00   0.0  0
 EG7  CONST_07  C11  N25  C13  C5      0.00   0.0  0
 EG7  CONST_08  C11  C8   C3   C5      0.00   0.0  0
 EG7  CONST_09  N25  C13  C5   C3      0.00   0.0  0
 EG7  CONST_10  N25  C11  C8   C3      0.00   0.0  0
 EG7  CONST_11  C10  C4   C1   C2      0.00   0.0  0
 EG7  CONST_12  C10  C9   C7   C2      0.00   0.0  0
 EG7  CONST_13  C13  C5   C3   C8      0.00   0.0  0
 EG7  CONST_14  C13  N25  C11  C8      0.00   0.0  0
 EG7  CONST_15  C14  N26  N27  C12     0.00   0.0  0
 EG7  CONST_16  N26  C14  C6   C12     0.00   0.0  0
 EG7  CONST_17  N27  C12  C6   C14     0.00   0.0  0
 EG7  CONST_18  CL1  C10  C9   C7    180.00   0.0  0
 EG7  CONST_19  CL1  C10  C4   C1    180.00   0.0  0
 EG7  CONST_20  C23  C7   C2   C1    180.00   0.0  0
 EG7  CONST_21  F32  C8   C3   C5    180.00   0.0  0
 EG7  CONST_22  F33  C9   C10  C4    180.00   0.0  0
 EG7  CONST_23  N29  C13  C5   C3    180.00   0.0  0
 EG7  CONST_24  C24  C11  C8   C3    180.00   0.0  0
 EG7  CONST_25  F33  C9   C7   C2    180.00   0.0  0
 EG7  CONST_26  C23  C7   C9   C10   180.00   0.0  0
 EG7  CONST_27  N29  C13  N25  C11   180.00   0.0  0
 EG7  CONST_28  N29  C14  C6   C12   180.00   0.0  0
 EG7  CONST_29  C24  C11  N25  C13   180.00   0.0  0
 EG7  CONST_30  C21  C12  C6   C14   180.00   0.0  0
 EG7  CONST_31  N26  N27  C12  C21   180.00   0.0  0
 EG7  CONST_32  F32  C8   C11  N25   180.00   0.0  0
 EG7  CONST_33  N29  C14  N26  N27   180.00   0.0  0
 EG7  CONST_34  H35  C1   C2   C7    180.00   0.0  0
 EG7  CONST_35  H58  N27  C12  C6    180.00   0.0  0
 EG7  CONST_36  H36  C2   C1   C4    180.00   0.0  0
 EG7  CONST_37  H38  C4   C1   C2    180.00   0.0  0
 EG7  CONST_38  H39  C5   C3   C8    180.00   0.0  0
 EG7  CONST_39  H37  C3   C8   C11   180.00   0.0  0
 EG7  CONST_40  H40  C6   C14  N26   180.00   0.0  0
 EG7  CONST_41  H60  O31  C15  C20   180.00   0.0  0
 EG7  Var_01    C19  N28  C18  C16   -60.44  30.0  1
 EG7  Var_02    N28  C18  C16  C20    58.35  30.0  1
 EG7  Var_03    C18  N28  C23  C7    -65.82  30.0  3
 EG7  Var_04    C13  N29  C14  C6    132.98  30.0  2
 EG7  Var_05    C14  N29  C13  C5   -177.26  30.0  1
 EG7  Var_06    N28  C23  C7   C2    111.54  30.0  2
 EG7  Var_07    C20  C24  C11  C8     91.18  30.0  2
 EG7  Var_08    H49  C21  C12  C6     91.44  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 EG7  chir_01  C19  N28  C17  C22  negativ
 EG7  chir_02  C20  C17  C24  C16  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 EG7  plan-1  C6   0.020
 EG7  plan-1  C12  0.020
 EG7  plan-1  C14  0.020
 EG7  plan-1  N26  0.020
 EG7  plan-1  N27  0.020
 EG7  plan-1  N29  0.020
 EG7  plan-1  H40  0.020
 EG7  plan-1  H58  0.020
 EG7  plan-1  C21  0.020
 EG7  plan-2  C7   0.020
 EG7  plan-2  C1   0.020
 EG7  plan-2  C4   0.020
 EG7  plan-2  C2   0.020
 EG7  plan-2  C9   0.020
 EG7  plan-2  C10  0.020
 EG7  plan-2  C23  0.020
 EG7  plan-2  F33  0.020
 EG7  plan-2  CL1  0.020
 EG7  plan-2  H35  0.020
 EG7  plan-2  H38  0.020
 EG7  plan-2  H36  0.020
 EG7  plan-3  C5   0.020
 EG7  plan-3  C3   0.020
 EG7  plan-3  C8   0.020
 EG7  plan-3  C11  0.020
 EG7  plan-3  C13  0.020
 EG7  plan-3  C24  0.020
 EG7  plan-3  N25  0.020
 EG7  plan-3  N29  0.020
 EG7  plan-3  H39  0.020
 EG7  plan-3  H37  0.020
 EG7  plan-3  F32  0.020
 EG7  plan-4  C15  0.020
 EG7  plan-4  C20  0.020
 EG7  plan-4  O31  0.020
 EG7  plan-4  H60  0.020
 EG7  plan-4  O30  0.020

